Organic solar cells are a potential low-cost alternative to conventional inorganic photovoltaics. The most successful organic solar cells rely on nanoscale phase separation between different components to achieve high efficiencies. Understanding and controlling nanoscale film structure has thus become the central challenge that affects every aspect of the field, from the optimization of new low-bandgap polymers to early efforts to scale up manufacturing of polymer solar cells. Our group has pioneered several scanning-probe methods, including time-resolved electrostatic force microscopy (trEFM) and photoconductive atomic force microscopy (pcAFM), as tools to characterize active organic solar cells. We discuss applications of these tools to study several model polymer systems, including the local origin of the photocurrent in polyfluorene blends, the effect of annealing on the formation of hole transport, electron transport and photocurrent collection networks in the archetypal polythiophene (P3HT) fullerene (PCBM) system, and the role that mesoscopic PCBM crystallites play in polyfluorene-copolymer/PCBM cells during solvent-vapor annealing. These data show the power of scanning-probe methods in correlating morphology with performance, and underscore the need to model these devices as fully 3D networks, rather than as uniform 2D semiconductor slabs.